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Biol111 Flashcards

1
Q

What can we use to understand the shape of hybridised orbitals ?

A

Balloon shape

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2
Q

What are the hybridised orbitals in water?

A

Sp3 hybridised ( 3p orbitals and these are the orbitals in O which are sharing with the H atoms)

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3
Q

What are the effects of hydrogen bonding in water molecules?

A

1) higher boiling point
2) ice floats
3) higher cohesion
4) high heat of vapourisation
5) higher surface tension
6) higher specific heat capacity
7) water is a goof solvent for polar molecules

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4
Q

When non-polar molecules are mixed with water, why do the non-polar molecules have a tendency to cluster?

A

To maximise the number of hydrogen bonds which cyan form

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5
Q

What are the 2 purine bases?

A

Adenine and Guanine

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6
Q

What are the pyrimidine bases?

A

Cytosine
Thymine
Uracil

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7
Q

What is a nucleoside composed of?

A

A base and a sugar

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8
Q

How many phosphate groups are ejected from nucleoside triphosphates to produce a nucleotide? What is this phosphate molecule called?

A

-2
-pyrophosphate

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9
Q

What direction is the DNA sequence always written in?

A

5’ to 3’

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10
Q

What did Watson and Crick analyse to determine the structure of DNA?

A
  • X-ray diffraction patterns from DNA fibres that Rosalind Franklin had taken
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11
Q

Which of the amino acid optical isomers are incorporated into proteins ?

A

The L-isomers

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12
Q

At pH 7 what state are the amino acids in?

A

They are zwitterions

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13
Q

Histadine’s side chain has a pea around what pH?

A

Physiological pH

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14
Q

PKa is the pH at which an ionisable group is one half charged and one half ……..
E.g …..% CH3COOH and ………%CH3COO-

A

Neutral

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15
Q

What is the rotation like around the peptide bond in a dipeptide? Why?

A

There is no rotation. It has double bond character due to the electron distribution.

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16
Q

Rotation around C alpha -C bond angle is denoted as what?
Rotation around N-C alpha is denoted as what ?

A

PSI
PHI

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17
Q

Rotation around C alpha -C bond angle is denoted as what?
Rotation around N-C alpha is denoted as what ?

A

PSI
PHI

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18
Q

Why are most combinations of PSI and PHI angles not allowed? What determines the shape of the entire protein?

A

Because of steric collisions between the side chains and the main polypeptide chain.

The values of the psi and phi angles for each amino acid determine the shape of the entire protein.

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19
Q

What is the main driving force in protein folding?

A

To attain an energetically stable structure

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20
Q

What are the 2 written ways of representing primary structure?

A
  • 3 letter abbreviations or single letter ones
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21
Q

Alpha helices are usually formed from how many amino acids?
How many amino acids are there per turn in an alpha helix ?
How many degrees does each amino acid turn the helix ?
What is the vertical distance from one amino acid to the next?
What is the pitch of the helix ( turn length ) ?

A

5-40
3.6
100 degrees
0.15nm
0.54nm

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22
Q

In the helical wheel diagram each residue is plotted …… degrees around a circle or spiral ?

A

100 degrees

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23
Q

With beta pleated sheets are they formed from non-continuous or continous regions ?
If the Beta strands line up in the same direction then the beta sheet is described as …….?
If the strands run in opposite directions then it is said to be ………?

A

Non-continuous
Parallel
Anti-parallel

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24
Q

With the parallel beta pleated sheet describe the hydrogen bonds? Anti-parallel?

A
  • hydrogen bonds are evenly spaced within the sheet
  • narrowly spaced H bond pairs separated by a larger gap
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25
Why are beta sheets often called pleated sheets?
- the carbon alphas lie successively above and below the plane of the sheet
26
What is the name of the region that links secondary structures? What are the highly flexible long loops called? What are the short loops called that connect anti-parallel beta strands ?
- loop regions - random coils - hairpin loops or beta turns
27
Why is proline found in loop regions ? Why is glycine often found in loops?
It introduces a kink into the polypeptide due to its locked ring structure Its small side chain enables it to form turns when other amino acids could not
28
How are parallel beta strands usually connected ?
By an alpha helix , the helix crosses the beta sheet from one edge to another, this is called a beta-alpha-beta motif
29
What term describes the process of adding sugars/carbs/glycans?
- glycosylation
30
What is the name of the molecule formed when 2 cysteine molecules combine? What do dilsulfide bridges do?
Cystine Make proteins more resistant to degradation and denaturation
31
What name is given to the complex which is composed of polypeptide subunits associating in a quaternary structure ?
Multimeric complex
32
What is a homodimer? What is a heterodimer?
- the same type of protein coming together and interacting with each other -2 different proteins interacting
33
What is a homodimer? What is a heterodimer?
- the same type of protein coming together and interacting with each other -2 different proteins interacting
34
What is haemoglobin composed of ?
4 polypeptides : 2 identical alpha chains and 2 identical beta chains
35
What is immunoglobin G? What is it composed of >
-A type of antibody -composed of 4 polypeptide chains and has intramolecular and intermolecular disulphide bridges
36
What are the 2 major classes of proteins ?
- globular ( chains arranged in compact domains ) - Fibrous proteins ( arranged into fibres and have a structural role)
37
What is the general function of globular proteins ? What is the general function of fibrous proteins ?
- active components of the cellular machinery - structural role
38
What are the 3 main groups of fibrous proteins ?
- coiled-coil ( keratin and myosin ) - Beta-sheets ( amyloid fibres and silks) - triple helix (collagens)
39
Are keratins durable? How many amino acids are in the repeat for keratin? Which residues (A-G) are hydrophobic and lie on the same side of the alpha helix? How is the coiled-coil formed ?
-Yes -7 -A and D - Two alpha-keratin helices twist around each other , associating via the hydrophobic faces of the helices. This forms a coiled-coil
40
In keratin the coiled-coil dimer then lines up with another to form a ………..? These tetramers are the building blocks of ……… which then form into protofibrils which form ……..
- staggered antiparallel tetramer -protofilaments - microfibrils
41
Fibroin 1 is produced by silkworms. How many amino acids are in the repeat? What is this repeat? Forms what? Glycine side chains project from one side and ….. and ……. Project from the other ?
6 -Gly-ser-gly-ala-gly-ala- An antiparallel beta sheet
42
Why is fibroin II really strong but still flexible?
- stretching would require the breaking of covalent bonds but it is flexible because the beta sheets are interacting via weak van de waals bonds
43
Nearly one third of the amino acids are ……. In collagen What are the other 2 amino acids ? What does collagen form instead of an alpha helix
-glycine -proline and hydroxyproline -forms a loose helix due to proline and hydroxyproline residues
44
3 collagen polypeptides form a …….. Which amino acid is the only one that can fit through teh centre of the triple helix? Which amino acids confer rigidity? What do the chains form ?
Triple helix Glycine Proline and Hydroxyproline Inter-chain hydrogen bonds
45
What is the basic formula of carbohydrates?
(CH2O)n
46
The simplest carbohydrates have one……. or ………… group and multiple hydroxyl groups
-aldehyde - Ketone
47
How many carbon atoms do monosaccharides usually have? What is a monosaccharide with 7 carbons called? If glyceraldehyde has 3 carbons and has an aldehyde group i.e it is an aldose. What term describes it?
3-7 Heptose Aldotriose
48
What form are most naturally occurring monosaccharides in? What is the formula for working out the number of isomers from a molecule with n chiral centres?
-D form -2 to the power of n
49
Aldehyde + alcohol ——-> Ketone + alcohol ———>
-hemiacetal -hemiketal
50
In solution, which type of monosaccharides form rings?
-pentoses and hexoses
51
Aldohexoses usually form ……… rings ? What is the asymmetric carbon at c-1 called on aldohexoses ? How many different anomers exist per molecule? In solution these anomers can interconvert via open chain form in a process known as what? For aldoses the anomeric carbon is always carbon ……?
Pyranose Anomeric carbon 2 , alpha and beta Mutarotation Carbon 1
52
What type of rings do ketohexoses usually form? What carbon is always the anomeric carbon?
Furanose rings Carbon 2
53
Give an example of a monosaccharide which forms both furanose and pyranose rings? (An aldose)
Ribose so anomeric carbon is always 1
54
Define a lipid
Lipids are a diverse group of naturally occurring molecules that are soluble in non-polar organic solvents such as chloroform (insoluble or poorly soluble in water)
55
Which muscle prefers fatty acids to glucose in terms of energy?
Heart and skeletal muscle
56
Why are fatty acids described as being ampphipathic?
They have 2 different chemical characteristics : a hydrophobic tail and a hydrophilic head
57
What 2 types of names do fatty acids have?
Trivial (e.g oleic acid) and systematic (e.g cis-9-octadecenoic acid)
58
What suffixes represent …… A) saturated B) Monounsaturated C) polyunsaturated
A) anoic B) enoic C) dienoic (2xC=C) trienoic (3x C=C)
59
A 16 carbon fatty acid is called what…..
Hexadecane (6+10)
60
What are the 2 classes of essential fatty acids? What is a common symptom of fatty acid deficiencies?
-omega-3 and omega-6 -Eczema
61
Why are plants a good source of EFAs ?
They possess the enzymes needed for their synthesis (e.g delta 12 and delta 15 desaturases) which can insert c=c bonds beyond carbon 9 in the chain
62
If fish are animals and animals cannot produce EFAs as they don’t have the necessary enzymes, why are fish a great source of EFAs (omega 3 fatty acids) ?
Fish eat micro algae , which are plants , the algae have the enzymes
63
Why are oils liquids at rip?
Packed with unsaturated fatty acids which have kinks in the chain so molecules are loosely packed so has a low melting point, so liquid at rtp.
64
What are ‘trans fats’ associated with ? Are naturally occurring fatty acids cis or trans?
Circulatory diseases Cis
65
6
66
What are the importances of biological membranes ?
-separate cell contents from surroundings -maintain different biochemical environments -selectively permeable
67
What was discovered in the 1915 about membranes? 1925? What was the sandwich model of membrane structure of 1935?
Contains lipids and proteins Bilayer of phospholipids Phospholipid bilayer between 2 layers of globular proteins
68
What was the 1972 model for membranes (the one upon which we have built upon today) ?
-fluid mosaic model- proteins inserted into the membrane sheltering the hydrophobic regions from water
69
What is the evidence for the fluid mosaic model?
Freeze fracture of membrane Protein bumps in the 2 layers
70
What type of movement occurs in phospholipids?
Predominantly lateral movement (really quickly) About once a month , a flip-flop movement (the 2 opposite phospholipids swap across the hydrophobic core)
71
How does cholestrol act as a temperature buffer in membranes >
High temp e.g 37 degrees - reduce movement Lower temps - prevents the phospholipids packing closely together to maintain fluidity
72
A membrane which is packed with unsaturated hydrocarbon tails is more/less fluid
More fluid
73
Do the proteins in the membrane move freely laterally? What experiment by Frye and Edidin was done in 1970?
Yes Fusion studies in mouse and human cells using different markers, proteins had moved between cells
74
What is “hop diffusion “ of proteins ?
To move to another area proteins have to ‘hop’ over actin cytoskeleton
75
What are the 3 main groups of proteins in the membrane?
-integral proteins (transmembrane) -peripheral proteins (loosely bound via other proteins) -lipid-anchored proteins
76
What is a function of membrane carbohydrates ?
-highly diverse -act as identity tags e.g blood groups are due to variation in carbohydrates
77
Membranes have distinct inside/outisde faces that differ in :
Lipid composition Peripheral proteins attached Carbs attached Integral proteins
78
Membranes are highly permeable to …………. And highly impermeable to………..
Small non-polar molecules and small uncharged ones Charged ions and large polar molecules
79
What are some of the other functions of membrane proteins?
-enzymatic activity -signal transduction -intercellular joining e.g gap and tight junctions -attachment to the cytoskeleton and extracellular matrix
80
Do optical isomers have the same chemical properties?
Yes, they only differ in the direction of rotated plane polarised light
81
Do optical isomers have the same chemical properties?
Yes, they only differ in the direction of rotated plane polarised light
82
Where does the glycosidic bond always form between monosaccharides?
Between the anomeric carbon of one sugar and the hydroxyl group of another.
83
What can the open chain forms of aldoses and ketoses do?
Reduce indicators such as Cu2+ to Cu+
84
In a disaccharide what is the non-reducing and the reducing end?
Non-reducing - anomeric carbon is linked in a bond so cannot mutarotate Reducing- not linked , sugar can mutarotate so it is a reducing sugar
85
What type of enzymes can join sugars together?
Glycosyltransferases
86
What term describes sugars with 1-5 carbons?
Oligosaccharides
87
Where does glycolysis take place? How many molecules of ATP are produced per glucose molecule ?
-cytosol of cell -2 molecules
88
How much of the energy stored in glucose is released in glycolysis ?
<25%
89
What is pyruvate converted to ? What does this molecule enter ?
Acetyl-coenzyme A Citric acid cycle
90
What is produced in the Krebs cycle/ citric acid cycle ?
3xNADH FADH2 2 x CO2 1xATP
91
How many enzymatic reactions (steps) are there in the citric acid cycle ?
8 steps
92
What are adipocytes ?
Fat storage cells
93
What are examples of compounds that are esterified with phosphate in phosphoglycerides?
Organic bases, amino acids , alcohols
94
What phenomenon is described ….? The internal and external faces of biological membranes are often composiotionally different
Membrane asymmetry
95
What is geometric isomerism
Same molecular formula but a different arrangement of the atoms in space cis trans
96
What functional group is thiol?
-SH
97
What are cysteine residues important in ?
Insulin’s quaternary structure
98
If at an amino acids side chains pka of 4 , 50% is protonated and 50% unprotonated what are the proportions at ph 5 and 3
Ph 3 = 90% is protonated Ph 5 = 10% is protonated
99
Give a few differences between globular and fibrous proteins?
Globular is soluble fibrous isn’t Globular is round but fibrous is chains Complex vs simple primary structure

Biol111 (1 decks)

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